CIRAD Dataverse
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921 research outputs found
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EURoot Maize
No full textThe data come from the EURoot DB Information System (IS).(http://euroot.cirad.fr/euroot/JSP/index.jsp). EURoot DB is the database of the EURoot project "Enhancing resource uptake from roots under stress in cereal crops". It manages information on QTLs, genes and mutants involved in root growth under stress (drought, low N or low P) in barley, durum wheat, maize and rice. This project funded by the European Comission and coordinated by CIRAD began on 1 January 2012 and ended on 31 December 2015. It was the topic KBBE.2011.1.2-05 - Root signalling, growth and development under abiotic stress conditions of the FP7-KBBE - Specific Programme "Cooperation": Food, Agriculture and Biotechnology. 19 Participants from various jeuropean countries were involved in this project.
The IS has a database per plant and the files of this dataset were extracted from the EURoot MAIZE database in tabulated text format. There is a file for each type of data which name includes the data type. Each line of a file has several columns describing the study (title, description, year, country, place, contact).
All publications concerning this dataset are recorded in the EUROOT_maize_references‧txt
TropGene Sugarcane
No full textThe data come from the TropGeneDB CIRAD information system (https://tropgenedb.cirad.fr/tropgene/JSP/index.jsp).
TropGeneDB contains data from studies on tropical and mediterranean plants for various kinds of topics such as marker, QTL, genotype, genetic, phenotype, cartography (genetic, physical and linkage disequilibrium maps), linkage disequilibrium, association and germplasm.
The plants concerned are banana, breadfruit, citrus, cocoa, coconut palm, cotton, oil palm, rice, rubber, sorghum and sugarcane.
The IS has a database per plant. The data were produced by CIRAD researchers or by CIRAD researchers and colleagues associated in research projects.
The SUGARCANE data in this dataset produced between 1987 and 2008 were extracted from the TROPGENE_SUGARCANE database in tabulated text format files. There is a file for each type of data which name includes the data type. Each line of a file has several columns describing the study (title, description, year, country, place, contact) it belongs to.
The tropgene_sugarcane_references‧txt file contains the references of the scientific publications on these data.
Files tropgene_sugarcane_images_markers_primerpairs‧txt and tropgene_sugarcane_images_traits‧txt contain the file names relative to some markers, primers or traits associated respectively to the study of genotypes and phenotypes. The images files are in the compressed file tropgene_sugarcane_images‧tar‧gz
"Parare-Arataye" permanent plots eighth census, 2022, Nouragues forest
No full textForest censuses from the Nouragues research station, CNRS, French Guiana, in the Guyafor network. This dataset gathered trees location, botanical identification and size measurement from the 2022 census. The mission of the Nouragues research Station is to foster scientific research in tropical rain forests, at a site remote from major human activities
sRNA dataset of Cavendish AAA non infected plant (BPO-60)
No full textDeep sequencing of sRNA from AAA non infected cavendish plant (BPO-60
Data for "Shifting trait coordination along a soil-moisture-nutrient gradient in tropical forests"
No full textThis dataset is the one analysed and discussed in the scientific paper "Shifting trait coordination along a soil-moisture-nutrient gradient in tropical forests" published in Functional Ecology. The aim of this work is to combine single-trait and trait syndrome approaches to evaluate how environmental filtering contributes to trees' chemical and water-related strategies in contrasted habitats of the tropical forest of French Guiana
A survey of spontaneous species and cover crop communities in an experimental banana fallow in Guadeloupe: densities and functional traits
No full textThis dataset was obtained from a vegetation survey conducted on an experimental improved fallow preceding a banana crop, in Guadeloupe, French West indies. In this experiment, 8 treatments that correspond to a combination of two practices (soil tillage and cover crop species) were tested on 5 blocks (repetitions). For each modality, one sown cover crop species (among three species tested) was combined with one soil tillage modality (among two modalities tested) to test the effect of these practices on the sponatenous vegetation. The spontaneous vegetation and the cover crops were monitored (species determination, densities/m²) on permanent quadrats (25cm x 25cm) each month for 12 months. Nine aboveground traits were measured at flowering peaks on the 12 most abundant species. Dynamic of height over the 12 months and some global descriptors of the community (biomass, cover rate) were also measured. For details on variables measurements, see the related published papers
Genotypic data, phenotypic data and GWAS summary statistics for 1129 triploid banana hybrids evaluated for 24 agro-morphological traits in Guadeloupe (2011-2016) and genotyped-by-sequencing for 200K single-nucleotide-polymorphism markers
No full textData include: (i) variant call format (VCF) for 1129 triploid banana hybrids from biparental crosses implying 38 M. acuminata accessions genotyped for 200K bi-allelic single nucleotide polymorphisms obtained by genotyping-by-sequencing, (ii) a table (TSV) presenting best linear unbiased prediction of genotypic effects for 24 agro-morphological traits evaluated between 2011 and 2020 at CIRAD Neufchateau station, Capesterre Belle-Eau, Guadeloupe, French West Indies (16°05’N, 61°35’W), along with pedigree information for 2727 triploid banana hybrids including the 1129 genotyped hybrids, (iii) an archive (TAR.GZ) of genome-wide association study summary statistics obtained from the standard K model, and (iv) an archive (TAR.GZ) of genome-wide association study summary statistics obtained from the Kc model with chromosome-specific kinships that aims at recovering statistical power at alleles carried by long non-recombined haplotypic segment
Initiation to R for survey data analysis : an example with the analysis of crop diversity in Subsaharan Africa
No full textThis initiation to survey data analysis with R was designed to be offered at a multi-stakeholders workshop within the EWA-BELT H2020 EU project (grant n°862848 ; ewabelt.eu).
This training had two main objectives :
The first objective was to do an initiation to data handling, cleaning, formatting and visualization with R from the very bases for people who never used R. This initiation to the basic concepts of R was also designed for people who already worked with R for statistical analysis but who did not have an introduction to the basics of R syntax and to the tidyverse syntax.
The second objective of this training was for partners to get familiar with the data collected during a survey about the diversity and valued of 'Neglected and Under-utilized Species' (NUS) in the frame of the EWA-BELT project.
In line with the first objective of the course, this training content can be used by any trainer for an initiation to R for very beginners wanting to be introduced to survey data cleaning, formatting and visualization or for people already introduced to R but who want to update there bases in R
Agent-based model SIT++ source code : Exploring the success of SIT with entomovectoring (boosted SIT) depending on insect pest and biocide characteristics.
No full textA generic model built in Netlogo to explore the features of insect pests and biocides that encourage the success of boosted SIT.
The model represents individuals of a same insect species, characterized by variables such as sex (male/female), developmental stage (immature/mature), age, health status. More specific characteristics are attributed depending of their sex.
The biocide used for the boosted SIT is defined by transmission routes and induced mortality.
The effects of conventional SIT and boosted SIT are compared on the same population to see if the additional aspect of entomovectoring is more effective in the management of the insect species.
See the ODD protocol in the associated publication for more details on variables and simulation design
Evidence for a gut microbial community conferring adaptability to abiotic and biotic stressors in phytophagous insects: the melon fruit fly Zeugodacus cucurbitae (Diptera:Tephritidae) as case study
No full textMicrobial symbionts are known to play a key role in the biology, ecology, and evolution of phytophagous insects, but their abundance and diversity are suggested to be influenced by environment stressors. In order to identify this hypothesis, the change in gut microbial community of laboratory and wild Z. cucurbitae strains under temperature, diet quality, and antibiotic treatment was assessed using 16S rRNA metabarcoding. Experiment was conducted between 2020 and 2021 using La Reunion population of Z. cucurbitae